scholarly journals Functional lability of RNA-dependent RNA polymerases in animals

2018 ◽  
Author(s):  
Natalia Pinzón ◽  
Stéphanie Bertrand ◽  
Lucie Subirana ◽  
Isabelle Busseau ◽  
Hector Escrivá ◽  
...  
Keyword(s):  
Rna Interference ◽  
Developmental Stages ◽  
Classical Model ◽  
Rna Polymerases ◽  
Model Organisms ◽  
Regulation System ◽  
Functional Diversification ◽  
Branchiostoma Lanceolatum ◽  
Silencing Pathways ◽  
Conserved Gene

AbstractRNA interference (RNAi) requires RNA-dependent RNA polymerases (RdRPs) in many eukaryotes, and RNAi amplification constitutes the only known function for eukaryotic RdRPs. Yet in animals, classical model organisms can elicit RNAi without possessing RdRPs, and only nematode RNAi was shown to require RdRPs. Here we show that RdRP genes are much more common in animals than previously thought, even in insects, where they had been assumed not to exist. RdRP genes were present in the ancestors of numerous clades, and they were subsequently lost at a high frequency. In order to probe the function of RdRPs in a deuterostome (the cephalochordate Branchiostoma lanceolatum), we performed high-throughput analyses of small RNAs from various Branchiostoma developmental stages. Our results show that Branchiostoma RdRPs do not appear to participate in RNAi: we did not detect any candidate small RNA population exhibiting classical siRNA length or sequence features. Our results show that RdRPs have been independently lost in dozens of animal clades, and even in a clade where they have been conserved (cephalochordates) their function in RNAi amplification is not preserved. Such a dramatic functional variability reveals an unexpected plasticity in RNA silencing pathways.Author summaryRNA interference (RNAi) is a conserved gene regulation system in eukaryotes. In non-animal eukaryotes, it necessitates RNA-dependent RNA polymerases (”RdRPs”). Among animals, only nematodes appear to require RdRPs for RNAi. Yet additional animal clades have RdRPs and it is assumed that they participate in RNAi. Here, we find that RdRPs are much more common in animals than previously thought, but their genes were independently lost in many lineages. Focusing on a species with RdRP genes (a cephalochordate), we found that it does not use them for RNAi. While RNAi is the only known function for eukaryotic RdRPs, our results suggest additional roles. Eukaryotic RdRPs thus have a complex evolutionary history in animals, with frequent independent losses and apparent functional diversification.

scholarly journals Genome-wide characterization of 2-oxoglutarate and Fe(II)-dependent dioxygenase family genes in tomato during growth cycle and their roles in metabolism

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shuo Wei ◽  
Wen Zhang ◽  
Rao Fu ◽  
Yang Zhang
Keyword(s):  
Metabolic Pathways ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Growth Cycle ◽  
Model Organisms ◽  
Gibberellin Biosynthesis ◽  
Type I ◽  
Multiple Model ◽  
Genome Wide ◽  
Tomato Growth

Abstract Background 2-Oxoglutarate and Fe(II)-dependent dioxygenases (2ODDs) belong to the 2-oxoglutarate-dependent dioxygenase (2OGD) superfamily and are involved in various vital metabolic pathways of plants at different developmental stages. These proteins have been extensively investigated in multiple model organisms. However, these enzymes have not been systematically analyzed in tomato. In addition, type I flavone synthase (FNSI) belongs to the 2ODD family and contributes to the biosynthesis of flavones, but this protein has not been characterized in tomato. Results A total of 131 2ODDs from tomato were identified and divided into seven clades by phylogenetic classification. The Sl2ODDs in the same clade showed similar intron/exon distributions and conserved motifs. The Sl2ODDs were unevenly distributed across the 12 chromosomes, with different expression patterns among major tissues and at different developmental stages of the tomato growth cycle. We characterized several Sl2ODDs and their expression patterns involved in various metabolic pathways, such as gibberellin biosynthesis and catabolism, ethylene biosynthesis, steroidal glycoalkaloid biosynthesis, and flavonoid metabolism. We found that the Sl2ODD expression patterns were consistent with their functions during the tomato growth cycle. These results indicated the significance of Sl2ODDs in tomato growth and metabolism. Based on this genome-wide analysis of Sl2ODDs, we screened six potential FNSI genes using a phylogenetic tree and coexpression analysis. However, none of them exhibited FNSI activity. Conclusions Our study provided a comprehensive understanding of the tomato 2ODD family and demonstrated the significant roles of these family members in plant metabolism. We also suggest that no FNSI genes in tomato contribute to the biosynthesis of flavones.

scholarly journals Anti-biofilm and Virulence Factor-Reducing Activities of Essential Oils and Oil Components as a Possible Option for Bacterial Infection Control

Planta Medica ◽  
2020 ◽  
Vol 86 (08) ◽  
pp. 520-537 ◽  
Author(s):  
Jürgen Reichling
Keyword(s):  
Quorum Sensing ◽  
Essential Oil ◽  
Essential Oils ◽  
Virulence Factor ◽  
Model Organisms ◽  
Regulation System ◽  
Expression Of Genes ◽  
Reporter Strains ◽  
Violacein Production ◽  
Essential Oil Compounds

AbstractPathogenic biofilm-associated bacteria that adhere to biological or nonbiological surfaces are a big challenge to the healthcare and food industries. Antibiotics or disinfectants often fail in an attempt to eliminate biofilms from those surfaces. Based on selected experimental research, this review deals with the potential biofilm-inhibiting, virulence factor-reducing, and biofilm-eradicating activities of essential oils and single essential oil compounds using Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, and Chromobacterium violaceum as model organisms. In addition, for the bacteria reviewed in this overview, different essential oils and essential oil compounds were reported to be able to modulate the expression of genes that are involved in the formation of autoinducer molecules, biofilms, and virulence factors. The anti-quorum sensing activity of some essential oils and single essential oil compounds was demonstrated using the gram-negative bacterium C. violaceum. Reporter strains of this bacterium produce the violet-colored compound violacein whose synthesis is regulated by quorum sensing autoinducer molecules called acylhomeserinlactones. Of great interest was the discovery that enantiomeric monoterpenes affected the quorum sensing regulation system in different ways. While the (+)-enantiomers of carvone, limonene, and borneol increased violacein formation, their (−)-analogues inhibited violacein production.For the successful eradication of biofilms and the bacteria living inside them, it is absolutely necessary that the lipophilic volatile substances can penetrate into the aqueous channels of biofilms. As shown in recent work, hydrophilic nano-delivery systems encapsulating essential oils/essential oil compounds with antibacterial effects may contribute to overcome this problem.

scholarly journals How Can Satellite DNA Divergence Cause Reproductive Isolation? Let Us Count the Chromosomal Ways

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Patrick M. Ferree ◽  
Satyaki Prasad
Keyword(s):  
Reproductive Isolation ◽  
Developmental Stages ◽  
Rapid Evolution ◽  
Model Organisms ◽  
Cellular Mechanisms ◽  
Closely Related Species ◽  
Heterochromatin Formation ◽  
Interspecies Hybrids ◽  
Postzygotic Reproductive Isolation ◽  
And Function

Satellites are one of the most enigmatic parts of the eukaryotic genome. These highly repetitive, noncoding sequences make up as much as half or more of the genomic content and are known to play essential roles in chromosome segregation during meiosis and mitosis, yet they evolve rapidly between closely related species. Research over the last several decades has revealed that satellite divergence can serve as a formidable reproductive barrier between sibling species. Here we highlight several key studies on Drosophila and other model organisms demonstrating deleterious effects of satellites and their rapid evolution on the structure and function of chromosomes in interspecies hybrids. These studies demonstrate that satellites can impact chromosomes at a number of different developmental stages and through distinct cellular mechanisms, including heterochromatin formation. These findings have important implications for how loci that cause postzygotic reproductive isolation are viewed.

Insect omics research coming of age1This review is part of a virtual symposium on recent advances in understanding a variety of complex regulatory processes in insect physiology and endocrinology, including development, metabolism, cold hardiness, food intake and digestion, and diuresis, through the use of omics technologies in the postgenomic era.

2012 ◽  
Vol 90 (4) ◽  
pp. 440-455 ◽  
Author(s):  
Bart Boerjan ◽  
Dries Cardoen ◽  
Rik Verdonck ◽  
Jelle Caers ◽  
Liliane Schoofs
Keyword(s):  
Rna Interference ◽  
Cold Hardiness ◽  
Model Organisms ◽  
Sequence Information ◽  
Huge Amount ◽  
Omics Technologies ◽  
Regulatory Processes ◽  
Biological Aspects ◽  
Insect Biology ◽  
Functional Inactivation

As more and more insect genomes are fully sequenced and annotated, omics technologies, including transcriptomic, proteomic, peptidomics, and metobolomic profiling, as well as bioinformatics, can be used to exploit this huge amount of sequence information for the study of different biological aspects of insect model organisms. Omics experiments are an elegant way to deliver candidate genes, the function of which can be further explored by genetic tools for functional inactivation or overexpression of the genes of interest. Such tools include mainly RNA interference and are currently being developed in diverse insect species. In this manuscript, we have reviewed how omics technologies were integrated and applied in insect biology.

Ontogenetic development of the otic region in the new model organism, Leucoraja erinacea (Chondrichthyes; Rajidae)

2018 ◽  
Vol 109 (1-2) ◽  
pp. 105-114 ◽  
Author(s):  
Cathrin PFAFF ◽  
Jürgen KRIWET ◽  
Kyle MARTIN ◽  
Zerina JOHANSON
Keyword(s):  
Soft Tissues ◽  
Developmental Stages ◽  
Model Organism ◽  
Model Organisms ◽  
Biological Research ◽  
Developmental Studies ◽  
Micro Computed Tomography ◽  
Computed Tomography Scanning ◽  
Cartilaginous Fishes ◽  
Tomography Scanning

ABSTRACTCartilaginous fishes have a long evolutionary history dating back 440 million years and include model organisms in a number of fields of biological research. However, comparative developmental studies of these organisms, particularly neuroanatomical investigations, still remain sparse. Here, pre-hatching to adult developmental stages of the Little Skate, Leucoraja erinacea, are investigated using micro-computed tomography scanning in conjunction with staining procedures designed to improve visualisation of soft tissues. Within the ear, the anatomy of the skeletal labyrinth changes during ontogeny and differs substantially from the underlying membranous system, contrary to previous observations in sharks. Additionally, substantial morphological remodelling characterises the parietal fossa, which appears initially as a massive and hook-like structure and subsequently becomes slender and surrounded by soft tissue. The sizes of the vestibular system and neurocranium increase isometrically from pre- to post-hatching phases, and then exponentially after the post-hatching stages.

Considering RNAi experimental design in parasitic helminths

Parasitology ◽  
2012 ◽  
Vol 139 (5) ◽  
pp. 589-604 ◽  
Author(s):  
JOHNATHAN J. DALZELL ◽  
NEIL D. WARNOCK ◽  
PAUL MCVEIGH ◽  
NIKKI J. MARKS ◽  
ANGELA MOUSLEY ◽  
...  
Keyword(s):  
Rna Interference ◽  
Experimental Design ◽  
Gene Function ◽  
Experimental Validation ◽  
Parasite Species ◽  
Model Organisms ◽  
Helminth Parasites ◽  
Parasitic Helminth ◽  
Parasitic Helminths ◽  
Parasite Biology

SUMMARYAlmost a decade has passed since the first report of RNA interference (RNAi) in a parasitic helminth. Whilst much progress has been made with RNAi informing gene function studies in disparate nematode and flatworm parasites, substantial and seemingly prohibitive difficulties have been encountered in some species, hindering progress. An appraisal of current practices, trends and ideals of RNAi experimental design in parasitic helminths is both timely and necessary for a number of reasons: firstly, the increasing availability of parasitic helminth genome/transcriptome resources means there is a growing need for gene function tools such as RNAi; secondly, fundamental differences and unique challenges exist for parasite species which do not apply to model organisms; thirdly, the inherent variation in experimental design, and reported difficulties with reproducibility undermine confidence. Ideally, RNAi studies of gene function should adopt standardised experimental design to aid reproducibility, interpretation and comparative analyses. Although the huge variations in parasite biology and experimental endpoints make RNAi experimental design standardization difficult or impractical, we must strive to validate RNAi experimentation in helminth parasites. To aid this process we identify multiple approaches to RNAi experimental validation and highlight those which we deem to be critical for gene function studies in helminth parasites.

scholarly journals ATP-binding Cassette Transporters Are Required for Efficient RNA Interference in Caenorhabditis elegans

2006 ◽  
Vol 17 (8) ◽  
pp. 3678-3688 ◽  
Author(s):  
Prema Sundaram ◽  
Benjamin Echalier ◽  
Wang Han ◽  
Dawn Hull ◽  
Lisa Timmons
Keyword(s):  
Rna Interference ◽  
Caenorhabditis Elegans ◽  
Abc Transporters ◽  
Transport Systems ◽  
Atp Binding ◽  
C Elegans ◽  
Steep Concentration Gradient ◽  
Conserved Gene ◽  
Membrane Transport Systems ◽  
Atp Binding Cassette

RNA interference (RNAi) is a conserved gene-silencing phenomenon that can be triggered by delivery of double-stranded RNA (dsRNA) to cells and is a widely exploited technology in analyses of gene function. Although a number of proteins that facilitate RNAi have been identified, current descriptions of RNAi and interrelated mechanisms are far from complete. Here, we report that the Caenorhabditis elegans gene haf-6 is required for efficient RNAi. HAF-6 is a member of the ATP-binding cassette (ABC) transporter gene superfamily. ABC transporters use ATP to translocate small molecule substrates across the membranes in which they reside, often against a steep concentration gradient. Collectively, ABC transporters are involved in a variety of activities, including protective or barrier mechanisms that export drugs or toxins from cells, organellar biogenesis, and mechanisms that protect against viral infection. HAF-6 is expressed predominantly in the intestine and germline and is localized to intracellular reticular organelles. We further demonstrate that eight additional ABC genes from diverse subfamilies are each required for efficient RNAi in C. elegans. Thus, the ability to mount a robust RNAi response to dsRNA depends upon the deployment of two ancient systems that respond to environmental assaults: RNAi mechanisms and membrane transport systems that use ABC proteins.

scholarly journals Neofunctionalization of embryonic head patterning genes facilitates the positioning of novel traits on the dorsal head of adult beetles

2016 ◽  
Vol 283 (1834) ◽  
pp. 20160824 ◽  
Author(s):  
Eduardo E. Zattara ◽  
Hannah A. Busey ◽  
David M. Linz ◽  
Yoshinori Tomoyasu ◽  
Armin P. Moczek
Keyword(s):  
Rna Interference ◽  
Embryonic Development ◽  
Gene Network ◽  
Evolutionary Novelty ◽  
Developmental Evolution ◽  
Flour Beetles ◽  
Novel Traits ◽  
Adult Head ◽  
Conserved Gene ◽  
Embryonic Head

The origin and integration of novel traits are fundamental processes during the developmental evolution of complex organisms. Yet how novel traits integrate into pre-existing contexts remains poorly understood. Beetle horns represent a spectacular evolutionary novelty integrated within the context of the adult dorsal head, a highly conserved trait complex present since the origin of insects. We investigated whether otd1/2 and six3 , members of a highly conserved gene network that instructs the formation of the anterior end of most bilaterians, also play roles in patterning more recently evolved traits. Using ablation-based fate-mapping, comparative larval RNA interference (RNAi) and transcript sequencing, we found that otd1/2 , but not six3 , play a fundamental role in the post-embryonic formation of the adult dorsal head and head horns of Onthophagus beetles. By contrast, neither gene appears to pattern the adult head of Tribolium flour beetles even though all are expressed in the dorsal head epidermis of both Onthophagus and Tribolium . We propose that, at least in beetles, the roles of otd genes during post-embryonic development are decoupled from their embryonic functions, and that potentially non-functional post-embryonic expression in the dorsal head facilitated their co-option into a novel horn-patterning network during Onthophagus evolution.

scholarly journals Comparative Genomics of NAD Biosynthesis in Cyanobacteria

2006 ◽  
Vol 188 (8) ◽  
pp. 3012-3023 ◽  
Author(s):  
Svetlana Y. Gerdes ◽  
Oleg V. Kurnasov ◽  
Konstantin Shatalin ◽  
Boris Polanuyer ◽  
Roman Sloutsky ◽  
...  
Keyword(s):  
De Novo ◽  
Physiological Role ◽  
Model Organisms ◽  
Special Importance ◽  
Nicotinamide Mononucleotide ◽  
Genomic Platform ◽  
Salvage Pathways ◽  
Conserved Gene ◽  
Key Aspects

ABSTRACT Biosynthesis of NAD(P) cofactors is of special importance for cyanobacteria due to their role in photosynthesis and respiration. Despite significant progress in understanding NAD(P) biosynthetic machinery in some model organisms, relatively little is known about its implementation in cyanobacteria. We addressed this problem by a combination of comparative genome analysis with verification experiments in the model system of Synechocystis sp. strain PCC 6803. A detailed reconstruction of the NAD(P) metabolic subsystem using the SEED genomic platform (http://theseed.uchicago.edu/FIG/index.cgi ) helped us accurately annotate respective genes in the entire set of 13 cyanobacterial species with completely sequenced genomes available at the time. Comparative analysis of operational variants implemented in this divergent group allowed us to elucidate both conserved (de novo and universal pathways) and variable (recycling and salvage pathways) aspects of this subsystem. Focused genetic and biochemical experiments confirmed several conjectures about the key aspects of this subsystem. (i) The product of the slr1691 gene, a homolog of Escherichia coli gene nadE containing an additional nitrilase-like N-terminal domain, is a NAD synthetase capable of utilizing glutamine as an amide donor in vitro. (ii) The product of the sll1916 gene, a homolog of E. coli gene nadD, is a nicotinic acid mononucleotide-preferring adenylyltransferase. This gene is essential for survival and cannot be compensated for by an alternative nicotinamide mononucleotide (NMN)-preferring adenylyltransferase (slr0787 gene). (iii) The product of the slr0788 gene is a nicotinamide-preferring phosphoribosyltransferase involved in the first step of the two-step nondeamidating utilization of nicotinamide (NMN shunt). (iv) The physiological role of this pathway encoded by a conserved gene cluster, slr0787-slr0788, is likely in the recycling of endogenously generated nicotinamide, as supported by the inability of this organism to utilize exogenously provided niacin. Positional clustering and the cooccurrence profile of the respective genes across a diverse collection of cellular organisms provide evidence of horizontal transfer events in the evolutionary history of this pathway.

scholarly journals Efficiency of RNA Interference in the Mouse Hematopoietic System Varies between Cell Types and Developmental Stages

2005 ◽  
Vol 25 (10) ◽  
pp. 3896-3905 ◽  
Author(s):  
Philipp Oberdoerffer ◽  
Chryssa Kanellopoulou ◽  
Vigo Heissmeyer ◽  
Corinna Paeper ◽  
Christine Borowski ◽  
...  
Keyword(s):  
Rna Interference ◽  
Gene Targeting ◽  
Developmental Stages ◽  
Cell Types ◽  
Gene Inactivation ◽  
Loss Of Function ◽  
Homologous Genes ◽  
Family Gene ◽  
Interfering Rna ◽  
Different Cell Types

ABSTRACT RNA interference (RNAi) is a naturally occurring posttranscriptional gene-silencing mechanism that has been adapted as a genetic tool for loss-of-function studies of a variety of organisms. It is more widely applicable than classical gene targeting and allows for the simultaneous inactivation of several homologous genes with a single transgene. Recently, RNAi has been used for conditional and conventional gene inactivation in mice. Unlike gene targeting, RNAi is a dynamic process, and its efficiency may vary both between cell types and throughout development. Here we demonstrate that RNAi can be used to target three separately encoded isoforms of the bcl-2 family gene bfl-1/A1 in a conditional manner in mice. The extent of gene inactivation varies between different cell types and is least efficient in mature lymphocytes. Our data suggest that RNAi is affected by factors beyond small interfering RNA-mRNA stoichiometry.

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